One species or four? Yes!...and, no. Or, Arbitrary assignment of lineages to species obscures the diversification processes
of Neotropical fishes

Stuart Willis

Species are fundamental units in many biological disciplines, but there is continuing
disagreement as to what species are, how to define them, and even whether the concept
is useful. While some of this debate can be attributed to inadequate data and insufficient
statistical frameworks in alpha taxonomy, an equal part results from the ambiguity
over what species are expected to represent by the many who use them. In many cases
the species “concept” acts as a red herring with regard to the identification of lineages
and their properties, serving to distract from our actual goal, which is to understand
the processes of diversification. One domain where this appears to be prevalent is
in resolution of the most lineage dense assemblage of vertebrates on Earth, Neotropical
freshwater fishes, which continue to be described under a paradigm presuming the structure
of meta-population lineages can be adequately described by discrete taxa, despite
ample empirical evidence that nature exhibits nested endemism and reticulate lineages
that are incongruent with the operational expectations of the “species” concept. As
a case study, I examined the delimitation of lineages in a “species complex” of “peacock
bass” cichlid fishes from the Amazon, the Cichla pinima sensu lato group, using extensive
molecular data. Although described in 2006 as four species based on highly variable
coloration patterns and overlapping meristics, these populations were later shown
to exhibit two non-sister mtDNA lineages that did not correspond to the described
species and which were haphazardly distributed geographically. In contrast, microsatellite
data showed extensive areas of both admixture between two clusters as well as areas
of no admixture. Finally, sequences from 17 nuclear genes recovered all the localities
of these species as monophyletic, in contrast with the mtDNA genealogy.

I re-examined these data in an integrated and quantitative manner to resolve their
contemporary and historical structure and their correspondence to “species”. The power
of the strategy applied here is that each of these apparent conundrums was largely
decipherable using model-based approaches that allowed testing of the apparent conflict
within and between datasets. A spherical phylogeographic analysis revealed that the
admixture represented in the microsatellite data result from a recent joint colonization
of the eastern Amazon by two non-sister lineages (“Southern” and “Western”) that evolved
allopatrically but that apparently did not develop intrinsic reproductive isolation.
The populations in the area recently colonized exhibit a hybrid ancestry that manifests
itself in their nuclear sequences and which is strong enough to affect a common ancestry
(monophyly) for the Southern and Western lineages under multi-species coalescent models.
Analyses of the microsatellite data with approximate Bayesian computation showed that
the degree and timing of admixture differs across these sub-populations, while FST-analogs
implied that this has been preserved by the low rates of contemporary gene exchange
between these eastern localities. Despite this extensive admixture, multi-species
coalescent-based delimitation with Bayes Factors not only recognized the separate
evolutionary history of the Southern and Western lineages even when these lineages
were reconstructed as monophyletic, but also emphasized the distinction of several
nested Western lineages that exhibit unique mtDNA sub-lineages. However, the mtDNA
and microsatellite data both confirmed that at least two of these western sub-lineages
have experienced recent gene exchange.

Although these analytical results provide a cohesive narrative for these lineages
in terms of the divergence, dispersal, and admixture processes that produced the current
pattern, it suggests that reconciliation of the evolutionary patterns of Cichla pinima
sensu lato with all but the most arbitrary definitions of “species” cannot be done
without ambiguity. Any of several renderings (one, two, or four species) would be
accurate with respect to divergence history and contemporary population structure,
but each would require subjective preference of criteria for conferring the species
rank and would obscure the processes that have contributed to this diversity. For
example, though the Southern and Western lineages had a separate evolutionary origin,
they apparently did not develop reproductive isolation. This characteristic would
not prevent their recognition as species under some concepts, but the result has been
that there are now a comparable number of admixed populations of these lineages as
unmixed and that they may now be functionally inseparable. On the other hand, recognizing
these as a single, hybrid species would ignore the ongoing diversification in the
western lineage. It would also treat each of the admixed populations as equal replicates
of the parental species, despite evidence that they are unique in the degree and age
of admixture, with presumably unique solutions for local adaptation. More broadly,
if these lineages are synonymized because of admixture or incomplete reproductive
isolation, what does this imply about the remaining species of Cichla, which exhibit
degrees of hybridization between both the closest and most distantly related species?

These results suggest that the historical narrative for these populations is more
complex than can be portrayed by recognizing them as one, two, or four species: their
history and contemporary dynamics cannot be unambiguously rendered as discrete units
(taxa) at any level without both choosing the supremacy of one delimitation criterion
and obscuring the very information that provides insight into the diversification
process. This calls into question the utility of species as a rank, term, or concept,
and suggests that while biologists may have a reasonable grasp of the structure of
evolution, our methods of conveying these insights need updating. The lack of correspondence
between evolutionary phenomena and “species taxa” should serve as a null hypothesis,
and researchers should focus on quantifying the diversity in nature at whatever hierarchical
level and in whatever form it occurs without the distraction of making a subjective
determination as to whether it can be captured by discrete taxa or rises to the rank
of “species”.